psfgen creates too many bonds in a distorted Fe4S4 cluster

From: Sibo Lin (sibolin_at_caltech.edu)
Date: Mon May 10 2010 - 22:50:00 CDT

I'm trying model a ferrodoxin protein with a distorted Fe4S4 cluster
(http://www.pdb.org/pdb/explore/explore.do?structureId=1IQZ). When I
try to create a psf file via VMD's psfgen commandline program, the
cluster comes out interconnected in the psf. Is there some way to
prevent this? I'm using topology and parameter files for Fe-S clusters
from Chris Chang's paper
(http://pubs.acs.org/doi/abs/10.1021/ct800342w), but upon minimization
the Fe4S4 cluster collapses rather than remain somewhat cube-like. I
think the extra bonds that psfgen defines may play a role in this.

Thanks,
-Sibo

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